A method for accurate inference of population size from serially sampled genealogies distorted by selection

Molecular Biology and Evolution

Volumn 28, Issue 11, 2011, Pages 3171-3181

  O'Fallon, Brendan D ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

coalescent; dengue; interference; selection; serial samples

Indexed keywords

ARTICLE; BAYES THEOREM; DENGUE; DENGUE VIRUS; GENEALOGY; NONHUMAN; POPULATION SIZE; PUERTO RICO; RNA VIRUS; SAMPLING; THAILAND;

BAYES THEOREM; DENGUE VIRUS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POPULATION DENSITY; PUERTO RICO; SELECTION, GENETIC; THAILAND;

DENGUE VIRUS;

EID: 80155146912     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr153     Document Type: Article

References (33)

1. Barton N, Etheridge AM. 2004. The effect of selection on genealogies. Genetics 166:1115-1131.
2. BartonN, Navarro A. 2002. Extending the coalescent to multilocus systems: The case of balancing selection. Genet. Res. 79:129-139.
3. Bazin E, Glemin S, Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312:570-572.
4. Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Munoz-Jordan JL, Pybus OG, Holmes EC, Gubler DJ. 2010. Epidemic dynamics revealed in dengue evolution. Mol. Biol. Evol. 27:811-818.
5. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, BeltranM, Vorndam V, Gubler DJ, McMillanWO. 2003. Selection-driven evolution of emergent dengue virus. Mol. Biol. Evol. 20:1650-1658
6. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, BeltranM, Vorndam V, Gubler DJ, McMillan WO. 2006. Molecular evolution of dengue 2 virus in Puerto Rico: Positive selection in the viral envelope accompanies clade reintroduction. J. Gen. Virol. 87:885-893.
7. Charlesworth B, MorganMT, CharlesworthD. 1993. The effect of deleterious mutation on neutral genetic variation. Genetics 134:1289-1303.
8. Comeron JM,Williford A, Kliman RM. 2008. The Hill-Robertson effect: Evolutionary consequences of weak selection and linkage in finite populations. Heredity 100:19-31.
9. Coop G, Griffiths R. 2004. Ancestral inference on gene trees under selection. Theor. Popul. Biol. 66:219-232.
10. Drummond A, Nicholls G, Rodrigo AG, Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
11. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
12. Drummond A, Rodrigo AG. 2000. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serialsample UPGMA. Mol. Biol. Evol. 17:1807-1815.
13. Felsenstein J. 1974. The evolutionary advantage of recombination. Genetics 78:737-756.
14. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, Mumford JA, Holmes EC. 2004. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327-332.
15. Gubler D. 1998. Dengue and dengue hemorrhagic fever Clin. Microbiol. Rev. 11:480-496.
16. HillWG, Robertson A. 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8:269-294.
17. Kingman JFC. 1982a. The coalescent. Stoch. Proc. Appl. 13:235-248.
18. Kingman JFC. 1982b. On the genealogy of large populations. J. Appl. Probab. 19A:27-43.
19. Maia L, Colato A, Fontanari JF. 2004. Effect of selection on the topology of genealogical trees. J. Theor. Biol. 226:315-320.
20. Neuhauser C, Krone SM. 1997. The genealogy of samples in models with selection. Genetics 145:519-534.
21. O'Fallon BD. 2010a. TreesimJ : A flexible forward time population genetic simulator. Bioinformatics 26:2200-2201.
22. O'Fallon BD. 2010b. A method to correct for the effects of purifying selection on genealogical inference. Mol. Biol. Evol. 27:2406-2416.
23. O'FallonBD, Seger J,Adler FR. 2010.Acontinuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Mol. Biol. Evol. 27:1162-1172.
24. Przeworski M, Charlesworth B, Wall JD. 1999. Genealogies and weak purifying selection. Mol. Biol. Evol. 16:246-252.
25. Rodrigo AG, Felsenstein J. 1999. Coalescent approaches to HIV population genetics. In: K. Crandall, editor. Molecular evolution of HIV. Baltimore (MD): Johns Hopkins University Press. p. 233- 272.
26. Rouzine IM, Coffin JM. 2006. Highly fit ancestors of a partly sexual haploid population. Theor. Popul. Biol. 71:239-250.
27. Seger J, Smith WA, Perry JJ, Hunn J, Kaliszewska ZA, La Sala L, Pozzi L, Rowntree VJ, Adler FR. 2010. Gene genealogies strongly distorted by weakly interfering mutations in constant environments. Genetics 184:529-545.
28. Slatkin M. 2008. A Bayesian method for jointly estimating allele age and selection intensity. Genet. Res. (Camb). 90:129-137.
29. Tajima F. 1989. Statisticalmethod for testing the neutralmutation hypothesis by DNA polymorphism. Genetics 123:585-595.
30. Twiddy SS, Holmes EC, Rambaut A. 2003. Inferring the rate and timescale of dengue virus evolution. Mol. Biol. Evol. 20:122-129.
31. Wakeley, J. 2008. Conditional gene genealogies under strong purifying selection. Mol. Biol. Evol. 25: 2615-2626.
32. Williamson S, Orive ME. 2002. The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evol. 19:1376-1384.
33. Zhang C,MammenMP, Chinnawirotpisan P, Klungthong C, Rodpradit P, Nisalak A, Nimmannitya S, Kalayanarooj S, Vaughn DW, Holmes EC. 2006. Structure and age of genetic diversity of dengue virus type 2 in Thailand. J. Gen. Virol. 87:873-883.